My friend James McClellan, a distinguished historian of science, likes ribbing me about my insistence that science’s glory days are over. In The End of Science I contended that science will keep extending and tweaking its current paradigms, like evolution by natural selection and the big bang, but there won’t be any more comparably profound “revelations or revolutions.” 

Jim enjoys rubbing my face in possible contradictions to my thesis. Recently he drew my attention to—and bought me a copy of, hard cover!—The Tangled Tree: A Radical New History of Life, by journalist David Quammen. The book’s blurb claims that our scientific view of life is undergoing a big shake-up. So I read the book. [*See Jim’s response to this column below.]

Quammen has a reputation as a terrific science writer, which turned out to be deserved. Tangled Tree is an epic tale about science’s quest to understand life. Quammen does for evolutionary biology what Dennis Overbye did for cosmology, the quest to understand the universe, in Lonely Hearts of the Cosmosone of my favorite science books. Both writers capture the thrills and messiness of research into nature’s deepest mysteries.

Just as Overbye’s story revolves around an obsessive, uncompromising curmudgeon, astronomer Alan Sandage, so does Quammen’s. His anti-hero is Carl Woese, inventor of a powerful molecular method for tracing evolutionary lineages. With it, Woese compiled evidence for a major new form of single-celled, prokaryotic life, Archaea, from which we may have descended.

Woese, who died in 2012 (and whom I interviewed in 1990 for an article on the origin of life), was a would-be revolutionary who thought he was under- and Darwin over-appreciated. He once wrote on a colleague’s manuscript, “You accord Darwin so much more substance than the bastard deserves.” Woese sought alternatives to natural selection as the major force underpinning evolutionary change, such as Stuart Kauffman’s concept of self-organized complexity (which I critiqued in End of Science).

Archaea are one of the “radical” findings that Quammen describes. Woese convinced many biologists that Archaea are so distinct from bacteria that they deserve their own label. But Archaea do not pose a challenge to Darwinian theory, our understanding of how species originate and evolve. I would compare Archaea to a revision in our model of galaxy formation in the early universe, which does not threaten the basic big-bang framework.

Horizontal gene transfer, the other discovery on which Quammen focuses, arguably does pose a challenge to conventional evolutionary theory. It involves different species passing genes directly to each other, usually via bacterial or viral infections. Tentative evidence for horizontal gene transfer emerged almost a century ago, but only in the past few decades have biologists recognized its influence on the evolution of multicellular organisms as well as Archaea and bacteria.

Horizontal gene transfer, Quammen asserts, “has overturned the traditional certitude that genes flow only vertically, from parents to offspring, and can’t be traded sideways across species boundaries.” Evolution has always been depicted by what Darwin called a “great tree,” with countless branches, representing different species, diverging from a common ancestor. The tree metaphor, it turns out, is inaccurate, or incomplete. Some branches are “tangled,” linked, by genes jumping from one species to another through horizontal gene transfer.

Scholars disagree on just how revolutionary horizontal gene transfer is. In 2000 W. Ford Doolittle reported on the implications of Archaea and horizontal gene transfer in Scientific American in “Uprooting the Tree of Life.” The “consensus tree” depicting evolution is “overly simplified,” Doolittle stated. A 2002 paper by Doolittle and others contended that horizontal gene transfer represents a “radical revision” of our view of life’s early history.

In 2009 New Scientist raised the stakes with a cover story about horizontal gene transfer, titled “Darwin Was Wrong.” A statement, not a question. A subtitle added “Cutting Down the Tree of Life.” (The online version of the article now has the softer headline “Why Darwin Was Wrong about the Tree of Life.”) In the article philosopher John Dupre called horizontal gene transfer “part of a revolutionary change in biology.” My italics.

In a rebuttal, “Darwin Was Right,” philosopher Daniel Dennett and biologists Richard Dawkins, Jerry Coyne and P.Z. Meyers called the New Scientist article “false” and “inflammatory.” “Nothing in the article showed that the concept of the tree of life is unsound,” they said, “only that it is more complicated than was realized before the advent of molecular genetics.”

Quammen, too, accuses New Scientist of sensationalism. Its headline may have “helped to sell magazines,” he comments, but it “caricatured the genuine challenge to Darwinian orthodoxy that the new discoveries raised.” Darwin “can’t be blamed” for not anticipating horizontal gene transfer, Quammen states. “He did the best he could, which was exceedingly well, with the evidence he could see.”

To answer the question posed in my headline: Nah. Far from being wrong, Darwin is as right as ever when it comes to his big idea, natural selection. He couldn’t foresee all the sources of variation within and between offspring, which provide the raw material on which natural selection operates. He didn’t know about genes, and he speculated, wrongly but reasonably, that acquired characteristics might be passed on to offspring, as Lamarck had proposed. (As Quammen notes, Lamarck’s hypothesis has undergone “small surges of reconsideration even down to the present day.”) 

Now we know that variations have many causes, including mutation, endosymbiosis, genetic drift, sexual recombination, epigenetic factors and, yes, horizontal gene transfer. But all variations, whatever form they take, serve as fodder for natural selection, which remains the primary evolutionary force, and which Darwin (and Wallace) discovered. 

Returning to the biology/cosmology analogy, evolution by natural selection and the big bang theory provide the basic frameworks for understanding life and the universe, respectively. Each paradigm constantly undergoes revisions and extensions. But just as the big bang theory absorbed the startling discovery two decades ago that the universe’s expansion is accelerating, so evolutionary theory has easily encompassed horizontal gene transfer.

Thomas Kuhn distinguished between “normal” science, which buttresses the prevailing paradigm, and “revolutionary” science, which overturns the paradigm. Horizontal gene transfer and Archaea represent normal science, which fleshes out Darwin’s revolutionary vision of life. All of biology since Darwin has been normal.

Carl Woese is hardly the only prominent modern thinker irked by Darwin’s dominance. Karl Popper was not a fan, and neither are philosopher Jerry Fodor and cognitive scientist Massimo Piattelli-Palmarini, authors of What Darwin Got Wrong (which I dismissed as “fatally flawed.”) But none of Darwin’s critics has done him any serious damage. Evolution by natural selection resembles capitalism. Both paradigms have an uncanny ability to absorb opposition, just as one microbe swallows another via endosymbiosis. 

That said, I find the discoveries on which Quammen reports fascinating. One subtheme of his book concerns how horizontal gene transfer might influence our self-conceptions. “What implications do these discoveries have for the concept of human identity?” Quammen asks. “What is a human individual? What are you?” Good questions. I just wrote a book about the quest to solve the mind-body problem, which asks, Who are we, really?

As Quammen reports, for every cell that is, strictly speaking, ours, our bodies contain roughly three bacterial cells—in our guts, mouths and elsewhere. Bacteria are much smaller than human cells and yet still account for as much as three percent of our total mass. About eight percent of our genome consists of “remnants of retroviruses that have invaded our lineage,” Quammen says. We are “mosaics.” We contain multitudes, and yet we are individuals. 

A final point, or rather, prediction, which I first made in The End of Science. No matter how much they learn, biologists will never really know how matter first became animate, just as cosmologists will never know how the universe began. Moreover, we will never find a final, definitive answer to the question of who we really are. Science-lovers should be grateful for the persistence of these mysteries. As long as they endure, so will our quest for self-knowledge.

*Here is James McClellan’s response to this column. For more on our ongoing argument about what Jim would call scientific “truth,” see also the introduction of my book Mind-Body Problems and the first three items in Further Reading.

Dear John,

I’m flattered that you again mention me in your wonderful blog, but reading your latest, “Was Darwin Wrong?,” gives me pause on two counts.

 First, you don’t address the epistemological status of current evolutionary theory. Even supposing you’re correct in all you say about evolution or about cosmology and the “end of science,” the implication that science has therefore determined unalterably true facts about nature is hardly self-evident or justified ipso facto. I thought for a while that you actually agreed with me that we are unable to escape the limitations of language and culture that box in any set of sentences we humans might utter, scientific or otherwise…that we are trapped in the chatter of us as slightly hairy apes trying to figure out our circumstances, but, alas, I see you are backsliding.

 (BTW, such a post-modernist take on science hardly excludes glory days ahead for science! The stories science tells are perhaps the greatest stories ever told and stunning testimony to human achievement. Who knows what lies ahead if we get a handle on dark matter, the origins of life, or even, pace Horgan, consciousness. Your “end of science” trope is too small-minded.)

 Secondly, I think Quammen is still correct that, all told, the successive discoveries surrounding Archaea, horizontal gene transfer, endosymbiosis, the microbiome and all the rest constitute a new view of life and a rewriting of the story of evolution, perspectives very different from those found in The Origin of Species. Put simply, changes in quantity have produced a change in quality, and in my view we live in a different world now regarding our understandings of life and its meanderings. “Natural selection” may still be a driver, but the context has changed fundamentally, and thus so also has the meaning of natural selection itself.

 Like you, I don’t see these changes as effecting a revolution per se, but what’s happened in recent decades is not Kuhnian “normal science” either. Scientists across a broad range of disciplines (genetics, taxonomy, paleontology, etc.) are not working out problems dictated by the Darwinian paradigm, they have made dramatic new discoveries in entirely new areas that have radically reframed that paradigm and the context in which to think about life and its history. There is grandeur in this new view of life, so why force it into the Procrustean bed of nineteenth-century theorizing?

Your friend, Jim

Further Reading:

Darwin Was Sexist, and So Are Many Modern Scientists

Science, History and Truth at the Faculty Club

Cantankerous Historian of Science Questions Whether Science Can Achieve “Truth” 

Thomas Kuhn Wasn't So Bad

Mind-Body Problems (free online book, also available as Kindle e-book and paperback)

Meta-Post: Posts on the Mind-Body Problem

Was I Wrong about “The End of Science”?

In Defense of Disbelief: An Anti-Creed

Science Will Never Explain Why There's Something Rather Than Nothing

Pssst! Don't tell the creationists, but scientists don't have a clue how life began